Due to their architectural features, ancient masonry churches are typically prone to seismic damages. Therefore, the social and cultural relevance of such structures requires the assessment of their seismic vulnerability, that is influenced by great halls, lack of a proper connection between the walls, and floor diaphragms not sufficiently rigid to allow a proper distribution of the seismic actions. In the present paper a case study is selected to assess the seismic vulnerability of a masonry church according to the conventional approach suggested by the Italian Guidelines on the evaluation and reduction of the seismic vulnerability of the Cultural Heritage. The Guidelines suggest a methodology characterized by increasing complexity of analysis. In detail, the first two levels of analysis are applied, assessing a qualitative analysis for evaluating the global seismic performance of the structure (LV1) and the local response of structural portions based on the macro-elements approach (LV2). The obtained results highlight the influence of the sensitivity of the technician opinion in applying the proposed methodology, since it is not certain that the less accurate approach is associated with a higher safety level, although it should be associated with greater uncertainties. Such occurrence verifies especially when the efficiency of the seismic protection devices is overestimated, and the effectiveness of the masonry toothing is underestimated.